SMTL ID : 5td5.1

Crystal Structure of Human APOBEC3B variant complexed with ssDNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

monomer

Ligands

1 x DT- DT- DC- DA- DT: DNA (5'-D(P*TP*TP*CP*AP*T)-3')(Non-covalent)

DT-DT-DC-DA-DT.1: 23 residues within 4Å: Chain A: I.21, G.22, R.23, H.24, K.25, T.26, N.52, H.57, A.58, I.83, W.85, S.86, P.87, C.88, I.116, Y.117, D.118, Y.119 Ligands: IOD.6, EDO.13, EDO.16, CL.18, IOD.19 Protein-ligand interaction information (PLIP) not available

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: H.57, C.88, W.91, C.93 Ligands: EDO.12, CL.18 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.57, A:C.88, A:C.93

9 x IOD: IODIDE ION(Non-functional Binders)

IOD.3: 5 residues within 4Å: Chain A: T.141, Y.142, E.167, S.170, Q.171 Ligand excluded by PLIP IOD.4: 2 residues within 4Å: Chain A: R.78, R.108 Ligand excluded by PLIP IOD.5: 4 residues within 4Å: Chain A: M.8, D.9, T.12, F.49 Ligand excluded by PLIP IOD.6: 4 residues within 4Å: Chain A: R.23, H.24 Ligands: DT-DT-DC-DA-DT.1, DT-DT-DC-DA-DT.1 Ligand excluded by PLIP IOD.7: 4 residues within 4Å: Chain A: A.172, L.173, R.176 Ligands: IOD.9 Ligand excluded by PLIP IOD.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain A: A.172 Ligands: IOD.7 Ligand excluded by PLIP IOD.10: 1 residues within 4Å: Chain A: G.134 Ligand excluded by PLIP IOD.19: 1 residues within 4Å: Ligands: DT-DT-DC-DA-DT.1 Ligand excluded by PLIP

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.11: 4 residues within 4Å: Chain A: W.91, Y.119, D.120, P.121 No protein-ligand interaction detected (PLIP) EDO.12: 8 residues within 4Å: Chain A: G.55, R.56, H.57, L.60, W.91, C.93 Ligands: ZN.2, EDO.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.57 Water bridges: A:R.56 EDO.13: 7 residues within 4Å: Chain A: H.57, W.91, Y.117, Y.119 Ligands: DT-DT-DC-DA-DT.1, DT-DT-DC-DA-DT.1, EDO.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.57, A:Y.117 Water bridges: A:G.55 EDO.14: 5 residues within 4Å: Chain A: V.137, L.177, R.178, L.181, Q.182 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.178 EDO.15: 6 residues within 4Å: Chain A: R.5, Y.6, Y.30, M.47, G.48, F.49 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.6, A:Y.30, A:F.49, A:F.49 EDO.16: 7 residues within 4Å: Chain A: N.19, G.20, I.21, G.22, W.85, R.115 Ligands: DT-DT-DC-DA-DT.1 No protein-ligand interaction detected (PLIP)

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.17: 1 residues within 4Å: Chain A: R.176 Ligand excluded by PLIP CL.18: 7 residues within 4Å: Chain A: H.57, A.59, P.87, C.88, C.93 Ligands: DT-DT-DC-DA-DT.1, ZN.2 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, K. et al., Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B. Nat. Struct. Mol. Biol. (2017)

Release Date

2016-12-28

Peptides

DNA dC->dU-editing enzyme APOBEC-3B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA dC->dU-editing enzyme APOBEC-3B